Yes, it's strange that it happened after the engine swap. But you have to eliminate one thing at a time or you'll never get anywhere. Just make sure to block the back tires so the car doesn't roll while you have the front wheels off the ground. If the brakes still lock up after removing the MC then you know that the problem is in the lines/heat. You didn't touch any of the brake lines, MC or anything AT ALL during the engine swap???
Treblig